In 2006, while scouting locations for his latest film, the Brazilian director José Padilha popped into his former university in Rio de Janeiro. "We got there, and everybody was smoking grass," he says. A year later, when Tropa de Elite (Elite Squad) was released in Brazil, the university's rector is unlikely to have been pleased with what he saw. Told through the eyes of a murderous special-forces police officer in Rio, the film offered a scathing critique of the city's middle and upper classes and fast became the most talked-about and controversial Brazilian film since 2002's City of God.

Elite Squad contains terrifying scenes of torture and execution and, perhaps for the first time in a major Brazilian film, drew a direct link between such violence and the excesses of upper-class university students like those smoking marijuana at Padilha's alma mater. "If you are a consumer of drugs in Rio, you know you are buying drugs from heavily armed groups that control poorer populations. You are choosing to finance those people," Padilha says.

Those who watch Elite Squad - which was exhaustively researched with help from former police officers and real-life drug traffickers - are left in little doubt as to where Rio's drugs come from or what, in Padilha's view, they result in. "The numbers are devastating. Just this year, in Rio, there were about 1,200 people killed by cops. To put this number in perspective: in the whole of the United States, a country with 300m people living in it, every year 200 people are killed by cops."

The films of 40-year-old Padilha have never made comfortable viewing for Brazilian society. In 1998, after a stint working as an investment banker, he began his film career by producing a documentary called The Charcoal People, telling the stories of exploited migrant workers forced to make charcoal in the Amazon rainforest.

Padilha's leap into the big time came in 2002 with another documentary, his directorial debut. Bus 174 delved into the background of a former street kid who became internationally famous after hijacking a bus in one of Rio's wealthiest boroughs, and subsequently died in custody.

What these films have in common, Padilha believes, is their examination of the "causal chains" behind social crises. In the case of Elite Squad, that meant looking at how society has created a police force that uses torture and killing to combat crime. Padilha, who is currently making a documentary for the BBC about Yanomami Indians in Venezuela, describes his work as a mixture of science and reportage. "We are reproducing what happens in places people don't look at, in an environment that people will look at, namely a [movie] theatre. Which is the same thing a journalist does - but the environment is a cafe, and the guy is holding a newspaper."

Uncovering this hidden world has earned Padilha his share of critics. In the wake of Elite Squad's release, sections of Brazil's left rounded on Padilha, arguing that the film promoted torture, while others described it as the work of a Trotskyite. "There is a tendency in Brazil - and in Latin America for that matter - that when you explain the psychology of a small-time criminal then you are a leftwinger, a communist trying to justify the crimes that this former street kid committed," he says. On the other hand if you explain why a killer cop is led to kill, "then you become a rightwinger. Since I did both, I am now never going to be elected."

Padilha's next film - a study of the murky world of Brazilian politics provisionally entitled The Corruptologist - also looks likely to have an explosive effect on the county's political scene, however. "The society here mistrusts the politicians even more than they mistrust the police. I think even the police mistrust the politicians. And I wonder why," he says. "The basic idea is: why is our political class like this? What is it that creates those politicians? It is the same thing as Elite Squad but in a different environment." Brasilia, you have been warned.